Cutting a Notch at the top a Rounded Cylinder
If you choose to go the route of booleans, then here is the method I would use.
Quad cap the cylinder to begin with. Delete the Ngon faces top and bottom, and grid fill them with Ctrl+F &gt; G with the edges selected.

Next you can add modifiers. Order is important, so here is the modifier stack:

Bevel and Weighted Normal are the key ones that help here, they will help eliminate alot of the shading issues that you will run into relying on boolean workflows.
Finally, enable Auto-Smooth in  Properties ‣ Object Data ‣ Normals


This is roughly the result you should end up with: